Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate H281DRAFT_05400 H281DRAFT_05400 isoquinoline 1-oxidoreductase, beta subunit
Query= metacyc::MONOMER-20833 (739 letters) >FitnessBrowser__Burk376:H281DRAFT_05400 Length = 749 Score = 413 bits (1062), Expect = e-119 Identities = 261/747 (34%), Positives = 401/747 (53%), Gaps = 55/747 (7%) Query: 14 LSRRRFL------ASTAVGALVIGFGLPLGAGRVQAATS---------AERGTQVP-AFL 57 +SRR FL + A G L++GF +P + +A S A+ G P AF+ Sbjct: 24 VSRRTFLKLSVTVGAAAGGGLLLGFSMPAVSQDQKAGKSVIGGDANEAAQNGVFAPNAFI 83 Query: 58 EIRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA-YVVMENGLR 116 +I G V L+ P +E GQG +T++ ++ EEL+ T ++ APP E + G + Sbjct: 84 QIDTAGKVTLVIPKVEMGQGVYTSIPMLIAEELEVPLDTVTLDHAPPDEKLFTDPLLGGQ 143 Query: 117 ITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYG 176 +TGGS S+R ++ MR+ GA AR +L+ A A+QW V + G+V+HAAS RS+GYG Sbjct: 144 LTGGSTSIRYAWEPMRKAGATARMLLIGAAAQQWQVDASSCHAKSGQVIHAASNRSIGYG 203 Query: 177 ELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAA 236 +L +A +PVP ++ L+DP F+ IG VKRLD+ +K G A + +D+++ +M++AA Sbjct: 204 QLVDAAAKLPVPQ--NVPLKDPKDFKIIGTAVKRLDSPEKVDGTATFGLDVRLPDMVYAA 261 Query: 237 VQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEA 296 + + P G + S+ + + + + GV V + AVAV+ + W AKR ++A+ + W E Sbjct: 262 IANCPVFGGKLASV-DDTNAKKIPGVRQVVKIDNAVAVIGDHTWAAKRGLQALDIKWNEG 320 Query: 297 A-ADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLN 355 A A +++ + D ++ R A++ +GDV A AKT+V+A Y +L Sbjct: 321 ADAKLSMKQIVDDLANASQRNGAVARK--------DGDVVHAFSNAKTRVDAVYQQPFLA 372 Query: 356 HAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRH 415 HA +EP + PDG EIWL +Q P R TGL +I +H+ L+GG FGR Sbjct: 373 HATMEPINCTVHVRPDGC-EIWLGSQVPTRVRDAAMAVTGLPADKIVVHNHLIGGGFGRR 431 Query: 416 FLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE 475 +D QA+ + K VS P+K++W+REE+ D+ RP K A LD G P+A + Sbjct: 432 LEFDMVT---QAVKIGKQVSTPVKVLWTREEDIQHDMYRPYYYDKISAGLDANGKPLAWQ 488 Query: 476 ------AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPML--- 526 ++ A P A K G +DP AVE S Y +PN+ + YV+ P Sbjct: 489 HRIVGSSIMARFAPP---AFKDG--LDPDAVEVASDLPYDLPNQLVD--YVRQEPHAIPT 541 Query: 527 GYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKR 586 +WR VG + F ESF+DELA + DP + R LL PR +L A + + Sbjct: 542 AFWRGVGPTRGTFVVESFIDELAAEAKVDPVKYRRDLLGKTPRALNVLNTAAQAANWGSA 601 Query: 587 GPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEA 646 P + RGV++ FGS+ A + +V+++ G+V V + A+D G +VNP VEA Sbjct: 602 VP------KGQGRGVSVMHAFGSYFAIVVDVAVDQGEVAVKRVVCAVDCGMVVNPNTVEA 655 Query: 647 QVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGE 706 QV G + G++ L E DG+ N+ Y +L + + V +V+S E GGIGE Sbjct: 656 QVQGGIIFGITAALYSEITIKDGRVEQNNFTDYRMLRIDETPPIDVHIVKSSEAPGGIGE 715 Query: 707 PPLPAVAPAVANAVAQLTGQRVRSLPL 733 P A+APA+ NA+ TG+R+R LP+ Sbjct: 716 PGTAALAPALTNAIFAATGKRLRQLPV 742 Lambda K H 0.317 0.134 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1341 Number of extensions: 71 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 749 Length adjustment: 40 Effective length of query: 699 Effective length of database: 709 Effective search space: 495591 Effective search space used: 495591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory